plot_insertions: Plots insertions using ggplot2.

In valenlab/amplican: Automated analysis of CRISPR experiments

Plots insertions using ggplot2.

Description

This function plots insertions in relation to the amplicon. Top plot is for the forward reads, middle one shows amplicon sequence, and bottom plot is for reverse reads.

Usage

plot_insertions(alignments, config, id, cut_buffer = 5, xlab_spacing = 4)

Arguments

alignments	(data.frame) Loaded alignment information from alignments_events.csv file.
config	(data.frame) Loaded table from config_summary.csv file.
id	(string or vector of strings) Name of the ID column from config file or name of multiple IDs if it is possible to group them. First amplicon will be used as the basis for plot.
cut_buffer	(numeric) Default is 5, you should specify the same as used in the analysis.
xlab_spacing	(numeric) Spacing of the x axis labels. Default is 4.

Value

(insertions plot) gtable object of insertions plot

See Also

Other specialized plots: metaplot_deletions(), metaplot_insertions(), metaplot_mismatches(), plot_cuts(), plot_deletions(), plot_heterogeneity(), plot_mismatches(), plot_variants()

Examples

#example config
config <- read.csv(system.file("extdata", "results", "config_summary.csv",
                               package = "amplican"))
#example alignments results
alignments_file <- system.file("extdata", "results", "alignments",
                               "events_filtered_shifted_normalized.csv",
                               package = "amplican")
alignments <- read.csv(alignments_file)
p <- plot_insertions(alignments, config, c('ID_1','ID_3'))

valenlab/amplican documentation built on Jan. 28, 2024, 5:10 a.m.